7-7617673-C-T

Variant names:

• chr7-7617673-C-T
• rs1557996

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.786 in 152,098 control chromosomes in the GnomAD database, including 47,984 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (47984 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119414 AN: 151980 Hom.: 47963 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.798

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.786 AC: 119486 AN: 152098 Hom.: 47984 Cov.: 31 AF XY: 0.789 AC XY: 58688 AN XY: 74336

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.797

Alfa AF: 0.837 Hom.: 72569

Bravo AF: 0.777

Asia WGS AF: 0.818 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1557996; hg19: chr7-7657304;